def test_slanepsample_paired_end_fastq_dir_fmt_validate_negative(self): filenames = ('paired_end_data/MANIFEST', 'metadata.yml', 'not-fastq.fastq.gz') for filename in filenames: filepath = self.get_data_path(filename) shutil.copy(filepath, self.temp_dir.name) format = SingleLanePerSamplePairedEndFastqDirFmt( self.temp_dir.name, mode='r') with self.assertRaisesRegex(ValueError, 'SingleLanePerSamplePaired'): format.validate()
def test_slanepsample_paired_end_fastq_dir_fmt_validate_positive(self): filenames = ('paired_end_data/MANIFEST', 'metadata.yml', 'Human-Kneecap_S1_L001_R1_001.fastq.gz', 'paired_end_data/Human-Kneecap_S1_L001_R2_001.fastq.gz') for filename in filenames: filepath = self.get_data_path(filename) shutil.copy(filepath, self.temp_dir.name) format = SingleLanePerSamplePairedEndFastqDirFmt( self.temp_dir.name, mode='r') format.validate()
def test_slanepsample_paired_end_fastq_dir_fmt_validate_missing_pair(self): filenames = ('single_end_data/MANIFEST', 'metadata.yml', 'Human-Kneecap_S1_L001_R1_001.fastq.gz') for filename in filenames: filepath = self.get_data_path(filename) shutil.copy(filepath, self.temp_dir.name) format = SingleLanePerSamplePairedEndFastqDirFmt(self.temp_dir.name, mode='r') with self.assertRaisesRegex(ValidationError, 'paired'): format.validate()
def test_slanepsample_paired_end_fastq_dir_fmt_validate_positive(self): filenames = ('paired_end_data/MANIFEST', 'metadata.yml', 'Human-Kneecap_S1_L001_R1_001.fastq.gz', 'paired_end_data/Human-Kneecap_S1_L001_R2_001.fastq.gz') for filename in filenames: filepath = self.get_data_path(filename) shutil.copy(filepath, self.temp_dir.name) format = SingleLanePerSamplePairedEndFastqDirFmt(self.temp_dir.name, mode='r') format.validate()
def test_slanepsample_paired_end_fastq_dir_fmt_validate_negative(self): filenames = ('paired_end_data/MANIFEST', 'metadata.yml', 'not-fastq.fastq.gz') for filename in filenames: filepath = self.get_data_path(filename) shutil.copy(filepath, self.temp_dir.name) format = SingleLanePerSamplePairedEndFastqDirFmt(self.temp_dir.name, mode='r') with self.assertRaisesRegex(ValueError, 'SingleLanePerSamplePaired'): format.validate()
def test_slanepsample_paired_end_fastq_dir_fmt_validate_missing_pair(self): filenames = ('single_end_data/MANIFEST', 'metadata.yml', 'Human-Kneecap_S1_L001_R1_001.fastq.gz') for filename in filenames: filepath = self.get_data_path(filename) shutil.copy(filepath, self.temp_dir.name) format = SingleLanePerSamplePairedEndFastqDirFmt( self.temp_dir.name, mode='r') with self.assertRaisesRegex(ValidationError, 'paired'): format.validate()